Albert mentioned how RNA Seq and proteomics can be used together. Today at AGBT Oxford nanopore announced that they will be selling an instrument that can sequence 50,000 - 100,000 base sequences of DNA (and theoretically directly sequence RNA as well). Check out the press release here. Given the low cost and rapid analysis times that they quote this could really revolutionize how we generate our protein reference libraries. These reads are long enough to cover complete RNA transcripts so we would know exactly what isoforms to include in our protein databases.

The truly exciting thing will be when they can use this nanopore technology to sequence proteins! Are mass spectrometers' days numbered?

The oxford nanopore technology is really interesting. I don't think it poses a threat for MS-based proteomics due to the way it detects proteins. Certainly the advantages it brings in sequencing experiments though offer a number of advantages to proteomics researchers, especially for improving the content of reference databases.